Table 1.

Genes up-regulated and down-regulated in ALDEFLUOR-positive populations

CategorySymbolDescriptionCytobandProbe set IDFunction
Up-regulatedGenes previously described to have a role in stem cell biologyTPRXLTetrapeptide repeat homeobox-likechr3p25.1239061_atEarly embryonic development
NOTCH2Notch homologue 2 (Drosophila)chr1p13-p11202443_x_atSelf-renewal program
RBM15RNA binding motif protein 15chr1p131555760_a_atDetermination of hematopoietic cell fate
ST3GAL3ST3 β-galactoside α-2,3-sialyltransferase 3chr1p34.11555181_a_atMaintenance of the embryonic antigens SSEA-3 and SSEA-4
NFYANuclear transcription factor Y, αchr6p21.3204107_atSelf-renewal program
PCNXPecanex homologue (Drosophila)chr14q24.2213173_atDetermination of neural cell fate of early developing embryo
SignalingFBXO21 *F-box protein 21chr12q24.22212231_atUbiquitination
WWOXWW domain containing oxidoreductasechr16q23.3-q24.1210695_s_atProtein degradation, transcription, and RNA splicing
CAMK2BCalcium/calmodulin-dependent protein kinase (CaM kinase) II βchr22q1234846_atCalcium signaling
PNPLA2Patatin-like phospholipase domain containing 2chr11p15.539854_r_atTriglyceride hydrolysis
CLIC5Chloride intracellular channel 5chr6p12.1-21.1213317_atChloride ion transport
UGCGL1UDP-glucose ceramide glucosyltransferase-like 1chr2q14.3222569_atProtein glucosylation
FBXL18F-box and leucine-rich repeat protein 18chr7p22.2220896_atUbiquitination
ADRBK1Adrenergic, β, receptor kinase 1chr11q1338447_atPhosphorylation of G protein-coupled receptors
SLC38A2Solute carrier family 38, member 2chr12q1559924_atNeutral amino acid transporter
Membrane proteinIL-8RA *Interleukin-8 receptor, αchr2q35207094_atInflammatory response
TAS2R14Taste receptor, type 2, member 14chr12p13241997_atBitter perception
CD300LBCD300 molecule-like family member bchr17q25.11554173_atImmune response
GIPC3GIPC PDZ domain containing family, member 3chr19p13.3236730_at
DNA repairRAD51L1RAD51-like 1 (S. cerevisiae)chr14q23-q24.21570166_a_atHomologous recombination repair
Chromatin remodelingARID1BAT rich interactive domain 1B (SWI1-like)chr6q25.1225181_atChromatin remodeling (SWI/SNF complex)
CytoskeletonEPPK1Epiplakin 1chr8q24.3208156_x_atMaintenance of the keratin intermediate filaments
Extracellular matrixCOL11A2Collagen, type XI, α2chr6p21.3216993_s_atSkeletal morphogenesis
KLK3Kallikrein 3, (prostate-specific antigen)chr19q13.41231629_x_atProtease
RNA interferenceEIF2C2Eukaryotic translation initiation factor 2C, 2chr8q24213310_atShort-interfering RNA-mediated gene silencing
UnknownZFP41Zinc finger protein 41 homologue (mouse)chr8q24.3227898_s_atUnknown
FAM49BFamily with sequence similarity 49, member Bchr8q24.21243182_atUnknown
PSORS1C2Psoriasis susceptibility 1 candidate 2chr6p21.3220635_atUnknown
Down-regulatedProtein synthesisMRPL42 *Mitochondrial ribosomal protein L42chr12q22217919_s_atProtein synthesis within the mitochondrion
MRPL54 *Mitochondrial ribosomal protein L54chr19p13.3225797_atProtein synthesis within the mitochondrion
Down-regulatedMRPL47 *Mitochondrial ribosomal protein L47chr3q26.33223480_s_atProtein synthesis within the mitochondrion
MRPS23 *Mitochondrial ribosomal protein S23chr17q22-q23223156_atProtein synthesis within the mitochondrion
EIF3S9 *eukaryotic translation initiation factor 3, subunit 9 η, 116 kDachr7p22.2236274_atInitiation of protein synthesis (EIF3 multiprotein complex)
SignalingALG5 *Asparagine-linked glycosylation 5 homologuechr13q13.3218203_atProtein glucosylation
DNAJC19 *DnaJ (Hsp40) homologue, subfamily C, member 19chr3q26.33225359_atImportation of mithochondrial protein
HBLD2 *HESB-like domain containing 2chr9q21.33221425_s_atIron-sulfur cluster biogenesis
GART *Phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetasechr21q22.1230097_atDe novo purine biosynthesis
NUP37 *Nucleoporin 37 kDachr12q23.2218622_atIntracellular protein transport across nuclear membrane
RNF7 *Ring finger protein 7chr3q22-q24224439_x_atSubunit of SKP1-cullin/CDC53-F box protein ubiquitin ligases
DC2 *DC2 proteinchr4q25223001_atProtein glycosylation
USP15 *Ubiquitin-specific peptidase 15chr12q14210681_s_atProtein degradation
COMMD6 *COMM domain containing 6-225312_atInhibition nuclear factor-κB signaling
UBL5 *Ubiquitin-like 5chr19p13.3218011_atUbiquitination
ApoptosisMRPL41 *Mitochondrial ribosomal protein L41chr9q34.3225425_s_atStabilization of p53 protein, cell cycle arrest [p21 (WAF1/CIP1) and p27 (Kip1) dependent]
PDCD10 *Programmed cell death 10chr3q26.1210907_s_atInitiation of apoptosis
PDCD5 *Programmed cell death 5chr19q12-227751_atInitiation of apoptosis
Differentiation programNACA *Nascent polypeptide-associated complex α polypeptidechr12q23-q24.1222018_atErythroid differentiation
Cell cycleFAM82B *Family with sequence similarity 82, member Bchr8q21.3218549_s_atRegulation of microtubule dynamic
RNA splicingCCNL1 *Cyclin L1chr3q25.321555411_a_atPre-mRNA processing
PRPF39 *PRP39 pre-mRNA processing factor 39 homologue (S. cerevisiae)chr14q21.3220553_s_atPre-mRNA processing
LSM3 *LSM3 homologue, U6 small nRNA associated (S. cerevisiae)chr3p25.1202209_atPre-mRNA processing
SFRS7 *Splicing factor, arginine/serine-rich 7, 35 kDachr2p22.1213649_atRegulation of RNA splicing
PRPF4B *PRP4 pre-mRNA processing factor 4 homologue B (yeast)chr6p25.2202127_atPre-mRNA processing
Oxidative phosphorylationATP5S *ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B)chr14q22.1206992_s_atSubunit of mitochondrial ATP synthase
NDUFA2 *NADH dehydrogenase (ubiquinone) 1α subcomplex, 2,chr5q31209224_s_atComponents of the complex I multisubunit enzyme
ATP5J2 *ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2chr7q22.1202961_s_atSubunit of mitochondrial ATP synthase
Down-regulatedIMMP1L *IMP1 inner mitochondrial membrane peptidase-likechr11p13230556_atProteolysis
UnknownASTE1 *Asteroid homologue 1 (Drosophila)chr3q22.1221135_s_atUnknown
MGC61571 *Hypothetical protein MGC61571chr3p24.1228283_atUnknown
WDR53 *WD repeat domain 53chr3q29227814_atUnknown
DKFZP686A10121 *Hypothetical proteinchr7q21.13234311_s_atUnknown
CHCHD8 *Coiled-coil-helix-coiled-coil-helix domain containing 8chr11q13.4220647_s_atUnknown
FLJ32745 *Hypothetical protein FLJ32745chr2q13235644_atUnknown
CHURC1 *Churchill domain containing 1chr14q23.3233268_s_atUnknown
XTP3TPA *XTP3-transactivated protein Achr16p11.2218069_atUnknown
FLJ37953 *Hypothetical protein FLJ37953chr2q33.1235181_atUnknown
SNORD50A *Small nucleolar RNA, C/D box 50Achr6q14.3244669_atUnknown
LOC644053 *Hypothetical protein LOC644053chr1q41235466_s_atUnknown
TMEM141 *Transmembrane protein 141chr9q34.3225568_atUnknown
C8orf59 *Chromosome 8 open reading frame 59chr8q21.2226165_atUnknown
  • NOTE: The 28 up-regulated genes in ALDEFLUOR-positive population (top) and the 42 down-regulated genes in ALDEFLUOR-positive population (bottom), common between the 413-gene and the 49-gene signatures (Supplementary Table S2). They are grouped together according to a common biological function and ranked according to their discriminating score (DS). DS was calculated for each gene as DS = (M1 − M2) / (S1 + S2), wherein M1 and S1 respectively represent mean and SD of expression levels of the gene in subgroup 1 and M2 and S2 in subgroup 2. Because of multiple hypotheses testing, confidence levels were estimated by 100 iterative random permutations of samples as previously described with a false positive rate of 1/1.000 ( 50). Underlined genes are cited in the text (Results and Discussion).

  • * Follows the name of genes found in the 49-gene signature.